| basecontent {Biostrings} | R Documentation |
WARNING: Both basecontent and countbases have been
deprecated in favor of alphabetFrequency.
These functions accept a character vector representing the nucleotide sequences and compute the frequencies of each base (A, C, G, T).
basecontent(seq) countbases(seq, dna = TRUE)
seq |
Character vector. |
dna |
Logical value indicating whether the sequence is DNA
(TRUE) or RNA (FALSE) |
The base frequencies are calculated separately for
each element of x.
The elements of x can be in upper case, lower case
or mixed.
A matrix with 4 columns and length(x) rows. The columns are
named A, C, T, G, and the values in each
column are the counts of the corresponding bases in the elements of
x. When dna=FALSE, the T column is replaced with
a U column.
R. Gentleman, W. Huber, S. Falcon
alphabetFrequency, reverseComplement
v<-c("AAACT", "GGGTT", "ggAtT")
## Do not use these functions anymore:
if (interactive()) {
basecontent(v)
countbases(v)
}
## But use more efficient alphabetFrequency() instead:
v <- DNAStringSet(v)
alphabetFrequency(v, baseOnly=TRUE)
## Comparing efficiencies:
if (interactive()) {
library(hgu95av2probe)
system.time(y1 <- countbases(hgu95av2probe$sequence))
x <- DNAStringSet(hgu95av2probe$sequence)
system.time(y2 <- alphabetFrequency(x, baseOnly=TRUE))
}